Guwapings, I got your E-Mail and then I saw this thread. The reason that the Wild Arms 2 battle menu in VGS 1.41 flickers, when using the FF9 patch, is because it is being forced to appear. VGS really can not display the menu w/out the patch. But something in the patch enables it to show the menu even though it flickers. The ficker is a reminder that the patch is enableing VGS to do something that it other wise couldn't.
For the fiickering in ePSXe, I would say Sunstorm's explanation makes perfect sense. The battle menu does not flicker for me, but then I have a GEForce card like he has. The difference is mine is a GEForce 2 GTS. But still, the menu has never fickered for me. So, you might want to consider what he said to fix your ePSXe flickering and unfortuneately you'll just have to tolerate the flickering in VGS, since there is nothing that can be done about it. Sorry.
sincerely,
sx/amiga